Students receive their GCSE results at Stoke Newington school and sixth form in London.
Photograph: Leon Neal/Getty Images

The proportion of pupils achieving good GCSE passes in England has fallen this year amid a confusing series of changes in exams and gradings, including a new nine-point scale in the key subjects of English and maths.

There were weaker results in history, maths and geography than last year, but the picture was complicated by changing patterns of entries and some substantial increases in numbers taking the tests as schools adjusted to the new process.

Overall, the proportion of students gaining at least a C, or a 4 under the new system, in England fell slightly, from 66.5% to 66.1%, but representatives of the examination boards said that in many subjects the results of older and younger pupils were affecting the national picture.

Much attention was focused on the first of the reformed GCSEs in England, with 51,000 entries awarded the new top grade of 9 in one of the three subjects they were offered – English language, English literature and maths.

The 9 grade was awarded to 3.5% of students in maths, 3.2% in English literature and 2.2% in English language. The exam regulator Ofqual estimated that around 2,000 pupils gained 9s in all three subjects. The 9 grade is set at a higher mark than the previous A* grade.

Among the lucky few achieving a clean sweep of top grades was Shannon Smith, a 16-year-old student at Our Lady’s school in Hackney, who admitted having had a nervous night before getting her results early on Thursday morning.

“I kept thinking about all the little mistakes I had made. The new system made me more nervous, especially for maths. It was overwhelming as we were the first year,” said Smith, who plans to take A-levels in English, maths and philosophy.

“The exam system is good, but there are some flaws. It is what it is. I have no control over it but just have to go through it.”

Another notable result was the A in chemistry awarded to Ines Alves, who escaped with her family from the Grenfell Tower fire the night before her exam, which she sat in the same clothes in which she had fled.

Ines Alves with her exam results on ITV’s This Morning. Photograph: Ken McKay/ITV/Rex/Shutterstock

But beyond the top grades, the national results were mixed, with slight falls overall in the proportion of pupils gaining a C or a 4 regarded as a good pass. The results were disappointing in geography and history but better in chemistry and biology.

Nick Gibb, the schools minister, hailed the figures as evidence that the new exams were translating into improved results. “The government’s new gold-standard GCSEs in English and maths have been benchmarked against the best in the world, raising academic standards for pupils. These reforms represent another step in our drive to raise standards, so that pupils have the knowledge and skills they need to compete in a global workplace,” he said.

However, the figures across England suggested that an influx of pupils taking English literature may have pulled down results in the top grades, as schools responded to new rules boosting their league table performance if pupils took both English language and literature exams.

Quick guide

The new GCSEs

What are the biggest changes to GCSEs?

The new courses have a greater emphasis on final exam marks, with little or no coursework counting towards final grades, and a new grading scheme running from 9 at the top to 1 as the lowest rank.

How does the new grading system work?

The new system sets a 4 as equivalent to a C under the previous rankings, while the top grades A* and A will be split into three grades, 7, 8 and 9 – with 9 awarded to those with marks at the top of the old A* grade.

Ofqual’s view

Ofqual’s chief regulator said the new courses allowed students to more fully display their abilities and knowledge, and would help them go on to further study. “In turn, the new 9 to 1 grade system signals to employers and others that this year’s students have studied new, more challenging content, and better differentiates between their achievements,” she said.

The NUT’s view

“Putting more emphasis on final exams is hitting hardest those who require the most support, such as disadvantaged students and students with special education need,” said Kevin Courtney, the union’s general secretary.

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At the same time, the government’s decision to drop an alternative exam, iGCSEs, from counting in league tables led to large number of schools switching back to having pupils take conventional GCSEs.

Exam board analysts said the net effect was to pull down the overall standard, meaning lower grades compared with previous years. The proportion of 16-year-olds in England achieving a 7 or above – equivalent to an A or above – fell from 21.7% to 19.1%.

In maths, where the number of entries was little changed, the proportion of 16-year-olds awarded a good pass of 4 rose to 70.7%, while those with a 7 or above was just a tick below 20%.

The new grade scheme of 9-1 will be gradually rolled across more subjects over the next two years. Next year pupils will sit the new exams in history, physics, biology and chemistry, along with most modern foreign languages.

There were also signs that funding shortages have forced schools to cut back on the number of subjects they offer. There were sharp falls in pupils taking religious studies, music and design and technology, which some attributed to the government’s English baccalaureate (Ebacc) herding schools into more academic subjects.

But modern foreign languages, which are part of the Ebacc suite of approved subjects, also failed to improve, with both French and German seeing falls of around 10% in entries, while the most popular subject, Spanish, was down by more than 3%.

“The reality is that many schools are now trapped between a rock and a hard place when deciding upon which subjects to offer students in the future,” said Paul Whiteman, general secretary of the National Association of Head Teachers.

“Many years of government reform have resulted in an absurd situation where school leaders are being pressured to choose between what is best for their school and what is best for pupils.”

Heads now face a nervous wait until the government’s official tables are published later this year, showing how well their school performed in a measure known as Progress 8, which compares the relative progress by pupils against the national average.

In Wales, the national GCSE results fell to their lowest level in a decade. The proportion of pupils gaining A*-C grades dropped to 62.8%, after staying at 66.6% since 2014.

Exam regulators in Wales said the drop was driven by an influx of younger pupils, as schools pushed pupils into taking some exams a year ahead of schedule.

Kirsty Williams, the Welsh education secretary, said the practice was unsustainable, and hinted at a ban. “I am concerned about the high number of pupils being entered early for their exams. Many of these pupils, who are taking exams before they have completed their two years of GCSE study, have not had the opportunity to reach their full potential,” Williams said.

In Northern Ireland, pupils outperformed their peers in England and Wales, with students’ A* to C grades rising by 0.4 percentage points overall.